The possibility of nominees for President that majorities do not seem to want is due to the plurality winner takes all elections and the existence of super-delegates in the Democratic Party.
If Trump wins the nomination, Republicans have another tool to block both his election and the Democratic nominee – the Electoral College.
Most states use plurality voting for electing members of the Electoral College. The Electoral College requires the person they designate as President to get a majority of electoral votes. If no one gets a majority, the House of Representatives gets to pick the President.
If the Libertarian Party nominee wins enough states to insure that no one gets a majority of the electoral votes, then if the Republicans can continue to hold the House of Representatives, the Establishment could end up selecting the President.
Could the Republican Establishment (whoever they are) give Gary Johnson or whoever wins the Libertarian nomination, enough votes to win a plurality in a sufficient number of states to deadlock the Electoral College?